LYNN - The Lynn man suspected of murdering a 3-month-old twin boy is a disabled US Army veteran who was having a “difficult time’’ accepting the news that he was not the father of the twin boys he once believed were his biological children, officials said.

Anthony Gideika, 33, pleaded not guilty in Lynn District Court to charges of assault and battery on a child causing serious bodily injury, but could face a charge of murder once the state medical examiner’s office establishes the cause of death for the infant, Essex County prosecutors said today.

Gideika is accused of assaulting Chase Gideika, who was pronounced dead at Massachusetts General Hospital on Tuesday where the infant was taken for treatment of a fractured skull, leg fractures, retinal bleeding, and bruising and swelling in the groin area.

Chase Gideika’s twin brother, Anthony Gideika Jr., was removed from the Gideika home on Western Avenue in Lynn by the state’s child protection agency, the Department of Children and Families, after the attack on his sibling.

According to Essex County prosecutors, DCF had previously removed a 3-year-old child from the Gideika home before the twins were born. DCF expressed concern that the mother and Gideika could not care for the children, who tested positive for methadone and benzodiazapan when they were born, prosecutors said. DCF received a report of neglect when the twins tested positive for drugs, prosecutors said.

A DCF spokeswoman today said the agency is reviewing a request from the Globe for a response to the prosecutors’ revelations about the DCF involvement with the Gideika family.

Gideika’s parents, a sister, and Jennifer Nelson, his girlfriend and mother of the children, attended the arraignment and left without speaking to reporters.

Also in court was Don Purrington, a peer specialist with the state Department of Veterans Affairs, who said he was with Gideika at a Veterans Administration hospital where Gideika was trying to get himself admitted.

Purrington said Gideika was a combat engineer during the three years he spent in the US Army between 2003 and 2006. Purrington said he could not disclose details of Gideika’s service, but said that combat engineers dismantle bombs, among other duties. Gideika is 100 percent disabled as a result of his military service, his attorney said.

“This happens more and more,’’ Purrington said of the incident of domestic violence. “By no means is that an excuse for what happened, but there are underlying issues that get self-medicated.’’

In court, Essex Assistant District Attorney Kate MacDougall said that Gideika recently learned he was not the father of Chase and Anthony and was having a “difficult time’’ with the news. In a Lynn police report filed in court, Gideika told police that “he has been having a rough time of it because he found out they weren’t his kids. Mr. Gideika stated that he did not take it out on Chase and that they were accidents.’’

She said that doctors who examined Chase Gideika at the North Shore Medical Center in Salem and at MGH in Boston had never seen another case where a child was abused so harshly.

Gideika called Lynn police around 2 a.m. Monday after Chase became unresponsive and was attempting mouth-to-mouth resuscitation on the child when police arrived. Gideika was described by police as “despondent” “unemotional” and with a “glazed over” expression during their interaction with him.

When police told Gideika they needed him to follow the infant to the hospital, he allegedly said, “Why? Was there something suspicious found or what?”

According to a police report and defense attorney Rebecca Whitehill of the Committee for Public Counsel Services, Gideika said he was sitting on the couch holding Chase Gideika on his lap when the doorbell rang on Saturday night.

Without thinking, Gideika said he jumped out of his seat, which sent Chase Gideika plunging downward onto a Kick and Play infant child toy. The infant bruised his genital area when he landed, straddle fashion, on a part of the infant’s toy, and then injured his head when the infant subsequently fell to the floor.

Gideika did not seek medical help immediately because “Chase did not cry hysterically so it did not strike him as that serious.’’

Nelson, the mother of the twins, was at a tattoo parlor and had left Gideika to care for the children, according to authorities.

Whitehill said that Gideika is adamant that he did not attack Chase Gideika and “denies this [was] anything other than accidental.’’

Bail was set at $100,00 cash.

Last year, the elder Gideika was convicted in Lynn District Court for drunken driving after his license was suspended and for giving police a false name when they finally stopped him, according to court records. At the time, he was under a “no drive” order that barred him from getting behind the wheel, records show.

He was arrested again on April 9, 2013, for operating under the influence after his license was suspended and spent nearly three months behind bars for that offense, records show.